Contacts of the helix formed by residues 154 - 168 (chain P) in PDB entry 3J7Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 154 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1639B U 3.4 32.5 - - - -
1640B A 3.5 4.7 - - - -
150P TRP 3.0 12.6 + - - -
151P GLU* 2.6 26.1 + - - -
152P ALA 3.6 2.1 - - - +
153P ALA* 1.3 81.2 - - - +
155P ASP* 1.3 64.0 + - - +
156P SER* 3.6 2.9 + - - -
157P MET* 3.2 19.8 + - - +
158P LYS* 3.4 18.7 + - - +
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Residues in contact with ASP 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1639B U 4.5 9.6 + - - -
1640B A 3.1 14.3 + - - +
121P VAL* 4.6 12.6 - - + -
153P ALA 4.2 4.3 - - - +
154P SER* 1.3 74.4 - - - +
156P SER* 1.3 60.5 + - - +
158P LYS* 3.2 13.4 + - - +
159P ARG* 2.9 37.0 + - + +
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Residues in contact with SER 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640B A 3.0 13.0 + - - -
84P ARG* 2.7 32.9 + - - -
121P VAL* 4.0 22.4 - - - +
124P CYS* 3.9 20.5 - - - +
151P GLU* 5.1 0.2 + - - -
154P SER* 3.6 5.2 + - - -
155P ASP* 1.3 76.9 - - - +
157P MET* 1.3 72.4 + - - +
159P ARG* 3.2 4.6 + - - +
160P LEU* 2.9 29.5 + - - +
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Residues in contact with MET 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P VAL* 3.8 34.5 - - + -
84P ARG* 4.0 16.8 - - + +
124P CYS* 4.7 7.0 - - + -
145P TYR* 2.9 29.6 - - + +
151P GLU* 3.2 39.5 - - + +
152P ALA* 4.8 1.8 - - - +
154P SER* 3.2 16.0 + - - +
155P ASP 3.2 0.2 - - - -
156P SER* 1.3 106.1 + - - +
158P LYS* 1.3 58.0 + - - +
160P LEU* 3.2 10.1 + - + +
161P GLN* 2.9 39.6 + - - +
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Residues in contact with LYS 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152P ALA 3.7 14.1 - - - +
153P ALA* 3.2 23.8 + - - +
154P SER 3.4 12.9 + - - +
155P ASP* 3.2 14.0 + - - +
157P MET* 1.3 77.4 - - - +
159P ARG* 1.3 57.4 + - + +
161P GLN* 3.2 16.3 + - - +
162P SER* 2.9 29.2 + - - -
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Residues in contact with ARG 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276 THR* 5.2 19.8 - - - +
121P VAL* 3.6 27.7 - - + +
122P VAL* 5.9 2.7 - - - +
125P GLU* 3.9 30.8 - - + +
155P ASP* 2.9 22.6 + - + +
156P SER* 3.2 8.5 + - - +
158P LYS* 1.3 76.7 - - + +
160P LEU* 1.3 58.7 + - - +
162P SER* 2.5 27.4 + - - -
163P ALA* 2.9 13.9 + - - +
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 4.2 22.9 - - + -
82P VAL* 4.3 15.9 - - + -
91P ALA* 5.0 4.5 - - + -
124P CYS* 4.5 9.9 - - + +
125P GLU* 4.6 6.4 - - - +
127P ILE* 5.9 0.2 - - + -
128P GLY* 3.3 28.7 - - - +
131P LEU* 4.8 6.7 - - + -
145P TYR* 4.3 15.3 - - + +
156P SER 2.9 12.6 + - - +
157P MET* 3.2 18.4 + - + +
159P ARG* 1.3 77.4 - - - +
161P GLN* 1.3 70.6 + - + +
163P ALA* 3.2 8.5 + - - +
164P MET* 2.9 42.6 + - + +
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Residues in contact with GLN 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145P TYR* 3.5 31.7 - - + -
152P ALA* 4.9 8.7 + - - +
157P MET* 2.9 25.8 + - - +
158P LYS* 3.4 19.1 - - - +
160P LEU* 1.3 80.0 - - + +
162P SER* 1.3 57.7 + - - +
164P MET* 3.2 4.4 + - - +
165P THR* 2.9 36.7 + - + +
171P LEU* 3.6 28.1 - - + +
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Residues in contact with SER 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLU* 4.6 4.2 + - - +
158P LYS 2.9 12.7 + - - -
159P ARG* 2.5 25.1 + - - -
161P GLN* 1.3 75.5 - - - +
163P ALA* 1.3 55.9 + - - +
165P THR* 2.4 27.8 + - - -
166P GLU* 2.9 31.0 + - - +
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Residues in contact with ALA 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLU* 3.3 25.6 - - - +
128P GLY 3.9 0.2 - - - -
129P ARG* 3.5 31.7 - - + +
132P ALA* 4.0 5.4 - - - +
159P ARG 2.9 5.9 + - - +
160P LEU 3.2 10.5 + - - +
162P SER* 1.3 82.2 + - - +
164P MET* 1.3 56.6 + - - +
166P GLU* 3.2 15.5 + - - +
167P GLY* 2.9 26.0 + - - -
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Residues in contact with MET 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 4.0 18.8 - - + -
128P GLY 3.4 22.4 - - - +
131P LEU* 4.0 13.7 - - + -
132P ALA* 3.8 11.1 - - - +
135P CYS* 3.9 9.6 - - - -
143P MET* 3.8 20.0 - - + -
160P LEU* 2.9 29.3 + - + +
161P GLN 3.2 8.3 + - - +
163P ALA* 1.3 76.4 - - - +
165P THR* 1.3 61.9 + - - +
167P GLY* 3.2 2.8 + - - -
168P GLY 3.0 18.5 + - - -
169P VAL* 3.2 50.4 + - + +
171P LEU* 4.3 7.9 - - + -
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Residues in contact with THR 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P GLN* 2.9 21.4 + - + +
162P SER* 2.4 31.2 + - - -
164P MET* 1.3 75.9 - - + +
166P GLU* 1.3 63.2 + - - +
168P GLY* 3.1 14.2 + - - -
169P VAL 4.1 12.5 + - - +
170P VAL* 6.0 2.0 - - - -
171P LEU* 5.2 7.6 - - + +
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Residues in contact with GLU 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLU* 4.3 4.8 - - - +
129P ARG* 3.8 28.9 + - + +
162P SER* 2.9 41.8 + - - +
163P ALA* 3.2 10.1 + - - +
165P THR* 1.3 79.1 + - - +
167P GLY* 1.3 63.3 + - - +
168P GLY* 3.4 0.9 + - - -
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Residues in contact with GLY 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ALA* 3.7 20.2 - - - -
133P GLN* 5.3 0.4 - - - -
136P LEU* 3.2 30.5 - - - +
163P ALA 2.9 10.7 + - - -
164P MET 3.2 5.1 + - - -
166P GLU* 1.3 79.1 - - - +
168P GLY* 1.3 56.4 + - - +
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Residues in contact with GLY 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P LEU* 3.5 10.5 - - - +
141P ASN* 3.9 13.9 - - - +
164P MET 3.0 2.8 + - - -
165P THR 3.1 11.3 + - - -
166P GLU 4.3 1.1 - - - -
167P GLY* 1.3 77.1 - - - +
169P VAL* 1.3 67.8 + - - +
170P VAL* 4.3 2.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il